Legacy Bioinformatics Scripts

These scripts are work fragments from my early bioinformatics analysis years, preserved in their historical form.

They reflect the analysis contexts, data formats, and engineering habits I had at the time. They are not presented as currently maintained software, nor as recommended modern implementations.

Source Archive

• Python scripts
  • PacBio processing tools: early scripts for PacBio / SMRT data organization, read extraction, and XML handling.
  • GTF annotation statistics
  • BLAST table span filter: filters BLAST tabular output by subject-coordinate span.
  • Miscellaneous scripts: code collection and crawler demos.
• Perl scripts
  • SAM / mpileup filters: scripts around mpileup, SAM, and PacBio read processing.
  • PacBio read extraction and adapter handling: scripts for CCS, subreads, selected reads, and adapter-related handling.
  • duplexes-related scripts: early utilities for small-RNA / read-pair analysis workflows.